Like said above your best bet is probably a new CDI.  When I rebuilt my Zilla from the ground up in 2010, I read for months on the QRQ site that closed.  The best bet was stay with OEM electrical stuff.  I purchased the Ricky Stator high output charging coils but they failed after a few months.  So, I scanned eBay for a few months buying used OEM electrical components until I had all spares for my 88 Zilla..... Coil, Stator, CDI, flywheel. 

I had the 2nd flywheel lightended, welded, and balanced.  That failed on me within a year.  I'm back to all stock OEM stuff that is 27 years old.  Knock on wood, they still work great.  If you can afford it and before the OEM decides to stop producing the part, you just can't go wrong with a new one.

I just found on Toledo's Parts finder that an 1988 CDI (PN#32900-01C00) has a MSRP of $510 but a selling price of $382.  Wow, that is actually cheaper then I thought it would be.  Forum members get a further discount too..... I would look into that if I was you.
http://www.hondaeasttoledo.net/OEMpartfinder.htm#/Suzuki_Motor_of_America%2c_Inc/LT500RL_%281988%29/ELECTRICAL/01720002/5601720017

If your still wanting to try used CDI's, I purchased my 2nd electrical set from "The Quadzilla Kings" on eBay in 2011.  I don't see any quadzilla electrical stuff for sale right now from them though.

When I received my 2nd electrical set, I swapped out to the new parts to make sure everything works as expected.  I still have the 2nd set in a box in the garage.  I was thinking about selling the set, but I think I would just rather keep it in case I decide to do another Zilla build and/or for backup purposes.

Good luck in your research and quad build.
Larry